Studies on individuals and animals with genetic variants in serotonin function shed light on the role of this neurotransmitter in behavior including the role of functional variants in serotonin genes in predisposing individuals to psychopathologies and to alcoholism. We are emphasizing the role of functional [candidate] alleles in behavior. Two 5-HT1A variants are rare amino acid substitutions (Gly22Ser and Val28Ile), one conservative and one nonconservative. The 5-HT2C variant is a common (allele frequency=0.18) nonconservative substitution (Cys23Ser). Two 5HT2A amino acid substitutions (Ala477Val and His452Tyr) have allele frequencies of 0.01 and 0.09. Rare serotonin transporter and 5-HT7 amino acid substitutions were also discovered. 5HT1A Gly22Ser when expressed in CHO-K1 cells dramatically altered desensitization and down regulation of these receptors. 5HT2C Cys23Ser in oocytes and COS-7 cells decreased ligand binding. 5HT2A His452Tyr impaired signal transduction in platelets from subjects with the 452Tyr allele. Recently a new TPH gene, TPH2, was detected and this gene encodes a brain-specific TPH. By resequencing, we identified an uncommon amino acid substitution in TPH2. A multilocus TPH2 haplotype was linked to suicidality in multiple populations, and to low levels of CSF 5HIAA, an index of brain serotonin turnover. A novel TPH2 missense allele reported and linked to depression by the Caron group could not be detected. Sib-pair linkage of 5HT1B, the terminal autoreceptor for serotonin neurons] to antisocial alcoholism was found in Finns and replicated in Southwestern American Indians [Lappalainen et al]. In a series of publications, we showed that the 5HT2A-1438 G>A promoter variant is linked to anxiety related conditions. These include OCD, seasonal affective disorder, anorexia nervosa and anxiety-related scales from the Tridimensional Personality Questionnaire. A 5HT5 amino acid substitution was detected and reveals a preliminary linkage signal to schizophrenia [Iwata et al]. The serotonin transporter (5-HTT) plays a critical role in the termination of serotonergic neurotransmission by Na-dependent uptake of serotonin by the presynaptic neuron and a functionally significant polymorphism in the 5-HTT promoter (HTTLPR) is the most studied locus in psychiatric genetics. The polymorphism affects in vitro 5-HTT transcription and, ultimately, 5-HTT function. We linked HTTLPR to the two anxiety related subscales of the TPQ in a sib pair analysis (C. Mazzanti), replicating the earlier finding by Lesch and colleagues. The variant was also linked to SAD [Enoch et al], alcohol response [Schuckit et al], and BPRS psychoticsm rating in schizophrenia [Malhotra et al]. The serotonin transporter polymorphism was next linked to two intermediate phenotypes in the causal chain connecting functional gene variant to behavior. These were midbrain serotonin transporter density determined by B-CIT SPECT [Heinz et al] and amygdala metabolic activity following a cognitive fear challenge [Hariri et al]. We discovered a new functional allele in HTTLPR and linked gain of function genotypes to OCD, in a large NIMH case/control dataset (D. Murphy) and a transmission disequilibrium dataset from the Univ. of Toronto consisting of parent-child trios (J. Kennedy). This new allele, an A>G SNP in the L allele, creates a functional AP2 site altering transcription. A rare serotonin transporter missense variant was also discovered in LNG, shown to be functional by NIMH colleagues, and studied in two families by collaborators in NIMH and at Western Psychiatric Institute. In these families, the HTT variant predicts a more severe behavioral syndrome which may include obsessionality, anxiety, and overt Asperger's syndrome.